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- PDB-8v51: Crystal structure of a HLA-B*35:01-NP10 with D1 TCR -

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Basic information

Entry
Database: PDB / ID: 8v51
TitleCrystal structure of a HLA-B*35:01-NP10 with D1 TCR
Components
  • Beta-2-microglobulin
  • D1 TCR alpha chain
  • D1 TCR beta chain
  • HLA-B35
  • LEU-PRO-PHE-GLU-LYS-SER-THR-VAL-MET
KeywordsIMMUNE SYSTEM / HLA B*3501 / NP418 epitope / T cell immunity / glycoprotein / host-virus interaction / immune response
Function / homology
Function and homology information


negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion ...negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
PHOSPHATE ION / HLA-B35 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.10000032944 Å
AuthorsLittler, D.R. / Rossjohn, J. / Gras, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Sci Immunol / Year: 2025
Title: Molecular determinants of cross-strain influenza A virus recognition by alpha beta T cell receptors.
Authors: Quinones-Parra, S.M. / Gras, S. / Nguyen, T.H.O. / Farenc, C. / Szeto, C. / Rowntree, L.C. / Chaurasia, P. / Sant, S. / Boon, A.C.M. / Jayasinghe, D. / Rimmelzwaan, G.F. / Petersen, J. / ...Authors: Quinones-Parra, S.M. / Gras, S. / Nguyen, T.H.O. / Farenc, C. / Szeto, C. / Rowntree, L.C. / Chaurasia, P. / Sant, S. / Boon, A.C.M. / Jayasinghe, D. / Rimmelzwaan, G.F. / Petersen, J. / Doherty, P.C. / Uldrich, A.P. / Littler, D.R. / Rossjohn, J. / Kedzierska, K.
History
DepositionNov 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA-B35
B: Beta-2-microglobulin
C: LEU-PRO-PHE-GLU-LYS-SER-THR-VAL-MET
D: D1 TCR alpha chain
E: D1 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,88512
Polymers93,3255
Non-polymers5607
Water8,017445
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.269, 46.155, 161.964
Angle α, β, γ (deg.)90.000, 101.402, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11D-450-

HOH

21D-501-

HOH

31D-515-

HOH

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein HLA-B35


Mass: 31527.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: B35:01 / Gene: B-3501 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O19626
#2: Protein Beta-2-microglobulin


Mass: 11690.058 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#4: Protein D1 TCR alpha chain


Mass: 21852.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV1*01 / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Protein D1 TCR beta chain


Mass: 27202.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV7-8*01 / Production host: Escherichia coli BL21(DE3) (bacteria)

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide LEU-PRO-PHE-GLU-LYS-SER-THR-VAL-MET


Mass: 1052.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Influenza A NP416 peptide H3N2 / Source: (synth.) Influenza A virus

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Non-polymers , 4 types, 452 molecules

#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→39.5 Å / Num. obs: 127751 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 30.4132591302 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Net I/σ(I): 8.6
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.28 / Num. unique obs: 12561 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.10000032944→39.5 Å / SU ML: 0.261758201977 / Cross valid method: FREE R-VALUE / σ(F): 1.33525364455 / Phase error: 25.6970406777
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.244254185972 3185 4.9921630094 %Random selection
Rwork0.21025193358 60615 --
obs0.211963469969 63800 99.7888480488 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.6421388436 Å2
Refinement stepCycle: LAST / Resolution: 2.10000032944→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6578 0 30 445 7053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01133408955136840
X-RAY DIFFRACTIONf_angle_d1.624290353929308
X-RAY DIFFRACTIONf_chiral_restr0.100698186801969
X-RAY DIFFRACTIONf_plane_restr0.006202754236471232
X-RAY DIFFRACTIONf_dihedral_angle_d23.10187545312514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1000004-2.13130.3080253208721210.2543629520732598X-RAY DIFFRACTION100
2.1313-2.16460.2502255866991290.24917763262639X-RAY DIFFRACTION100
2.1646-2.20010.3126180369281250.2559403074542674X-RAY DIFFRACTION100
2.2001-2.23810.3792705701251470.3596683254232495X-RAY DIFFRACTION97.9970326409
2.2381-2.27880.4425336899041470.4250927089332563X-RAY DIFFRACTION98.2239942008
2.2788-2.32260.3609564417621630.2912249384072584X-RAY DIFFRACTION99.4569152788
2.3226-2.370.3209542014751420.2434685439232619X-RAY DIFFRACTION100
2.37-2.42150.296104109931390.2307434295272634X-RAY DIFFRACTION100
2.4215-2.47790.2674127748281210.228538474572617X-RAY DIFFRACTION100
2.4779-2.53980.2936623092681390.220141009772621X-RAY DIFFRACTION100
2.5398-2.60850.2572317153361330.2262919055432637X-RAY DIFFRACTION100
2.6085-2.68520.3024720312831230.2229101555622613X-RAY DIFFRACTION100
2.6852-2.77190.2636026729521330.2237546059622634X-RAY DIFFRACTION100
2.7719-2.8710.2332324735611470.21554853942671X-RAY DIFFRACTION100
2.871-2.98590.2414524630541570.2210652952952598X-RAY DIFFRACTION100
2.9859-3.12180.2639162871841370.2165829251682624X-RAY DIFFRACTION100
3.1218-3.28630.2311435811591330.2055456308652665X-RAY DIFFRACTION100
3.2863-3.49210.226252040251670.1955374817622631X-RAY DIFFRACTION100
3.4921-3.76170.2411419306431270.1930161276952651X-RAY DIFFRACTION99.964015833
3.7617-4.140.2026854075831330.1802780779112669X-RAY DIFFRACTION100
4.14-4.73860.1809712509011470.15691018892679X-RAY DIFFRACTION100
4.7386-5.96820.201432878031270.1656229264462714X-RAY DIFFRACTION100
5.9682-39.50.2001360480411480.1976655258592785X-RAY DIFFRACTION99.5587236931
Refinement TLS params.Method: refined / Origin x: 14.0028419592 Å / Origin y: -14.226634744 Å / Origin z: 22.306921703 Å
111213212223313233
T0.108831921757 Å2-0.0272855685361 Å2-0.0186914588231 Å2-0.091701400799 Å20.00683659408404 Å2--0.128674194013 Å2
L0.321778854603 °2-0.0641247904446 °2-0.293136171445 °2-0.252823364764 °20.209028258092 °2--0.696899994491 °2
S-0.0101038067041 Å °0.0193512541769 Å °-0.0269138518981 Å °-0.00613814912326 Å °-0.0321249330403 Å °0.0560752586559 Å °0.0576150098183 Å °-0.0809138183318 Å °-0.118959769886 Å °
Refinement TLS groupSelection details: all

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